multimodal-dimelo

Code to accompany the manuscript Integrated analysis of multimodal long-read epigenetic assays (Marcus, Dixon-Luinenburg et al.)

Installation

Clone this repo:

git clone https://github.com/streetslab/multimodal-dimelo

Create your conda environment with the necessary conda dependencies:

conda env create -f environment.yml

Note: Instead of installing the environment in this directory, you can use the --prefix argument to create the environment in a specified location. You can then symlink it to your conda home folder. This may be useful for installation on cluster systems with limited user permissions.

# OPTIONAL FOR SOME HPC CONFIGURATIONS
conda env create -f environment.yml --prefix /PATH/TO/CUSTOM/LOCATION
ln -s /PATH/TO/CUSTOM/LOCATION /home/user/conda/envs/multimodal_dimelo

Activate the conda environment:

conda activate multimodal_dimelo

Install python dependencies and this package with pip. This will bring in the latest dimelo package as well as some other required libraries:

pip install .

Installation and configuration of external tools

Download and/or install the following:

• UCSC tools
  • liftOver
  • bigWigToBedGraph
  • bedGraphToBigWig
• bedtools
• samtools

To configure this repository to reflect your working environment, first copy the example configuration file:

cp config.toml.example config.toml

Then open config.toml and update the empty entries with appropriate paths to the executables for your system (e.g. /usr/bin/bedtools)

Obtaining data

Basecalled and aligned data in BAM format from this study are currently available by request; see the manuscript for details.

Downloaded BAM files should be placed in multimodal-dimelo/data/processed.

Running analysis

To regenerate the figures for this manuscript, first run third_party_data.ipynb to download all necessary data and perform necessary processing to generate reference files (e.g. BEDs).

Then run any of the analysis notebooks in any order:

1. CTCF_analysis.ipynb
2. LMNB1_analysis.ipynb
3. crosstalk_analysis.ipynb
4. motif_analysis.ipynb